MZminePreferences.java

/*
 * Copyright 2006-2015 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.gui.preferences;

import java.text.DecimalFormat;

import javax.annotation.Nullable;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Element;

import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.BooleanParameter;
import io.github.mzmine.parameters.parametertypes.OptionalModuleParameter;
import io.github.mzmine.parameters.parametertypes.filenames.FileNameParameter;
import javafx.scene.control.ButtonType;

public class MZminePreferences extends ParameterSet {

  private final Logger logger = LoggerFactory.getLogger(this.getClass());

  public static final NumberFormatParameter mzFormat = new NumberFormatParameter("m/z value format",
      "Format of m/z values", "Number formatting", false, new DecimalFormat("0.0000"));

  public static final NumberFormatParameter rtFormat =
      new NumberFormatParameter("Retention time format", "Format of retention time values",
          "Number formatting", false, new DecimalFormat("0.00"));

  public static final NumberFormatParameter intensityFormat =
      new NumberFormatParameter("Intensity format", "Format of intensity values",
          "Number formatting", true, new DecimalFormat("0.0E0"));

  public static final NumOfThreadsParameter numOfThreads = new NumOfThreadsParameter();

  public static final OptionalModuleParameter proxySettings = new OptionalModuleParameter(
      "Use proxy", "Use proxy for internet connection?", "Proxy", new ProxySettings());

  public static final FileNameParameter rExecPath = new FileNameParameter("R executable path",
      "Full R executable file path (If left blank, MZmine will try to find out automatically). On Windows, this should point to your R.exe file.",
      "R support", (value, messages) -> {
        if (value == null)
          return true;
        if (!value.exists()) {
          messages.add("File does not exist");
          return false;
        }
        if (!value.canExecute()) {
          messages.add("File is not executable");
          return false;
        }
        return true;

      }, FileNameParameter.Type.OPEN);

  public static final BooleanParameter sendStatistics = new BooleanParameter("Send statistics",
      "Allow MZmine to send anonymous statistics on the usage of its modules?", "Statistics", true);

  // public static final WindowSettingsParameter windowSetttings = new
  // WindowSettingsParameter();

  public MZminePreferences() {
    super(mzFormat, rtFormat, intensityFormat, numOfThreads, proxySettings, rExecPath,
        sendStatistics);
  }

  @Override
  public ButtonType showSetupDialog(@Nullable String title) {

    ButtonType retVal = super.showSetupDialog(title);
    if (retVal == ButtonType.OK) {

      // Update system settings
      updateSystemSettings();

      // Repaint windows to update number formats
      // TODO: MZmineCore..getDesktop().getMainWindow().repaint();
    }

    return retVal;
  }

  public void loadValuesFromXML(Element xmlElement) {
    super.loadValuesFromXML(xmlElement);
    updateSystemSettings();
  }

  private void updateSystemSettings() {

    // Update system proxy settings
    Boolean proxyEnabled = getParameter(proxySettings).getValue();
    if ((proxyEnabled != null) && (proxyEnabled)) {
      ParameterSet proxyParams = getParameter(proxySettings).getEmbeddedParameters();
      String address = proxyParams.getParameter(ProxySettings.proxyAddress).getValue();
      String port = proxyParams.getParameter(ProxySettings.proxyPort).getValue();
      System.setProperty("http.proxySet", "true");
      System.setProperty("http.proxyHost", address);
      System.setProperty("http.proxyPort", port);
    } else {
      System.clearProperty("http.proxySet");
      System.clearProperty("http.proxyHost");
      System.clearProperty("http.proxyPort");
    }

    NumOfThreadsValue numOfThreadsValue = getParameter(numOfThreads).getValue();
    if (numOfThreadsValue != null) {
      int threadPoolSize = numOfThreadsValue.getNumberOfThreads();
      int currentThreadPoolSize = MZmineCore.getTaskExecutor().getCorePoolSize();
      if (threadPoolSize != currentThreadPoolSize) {
        logger.debug("Setting the thread pool size to " + threadPoolSize);
        MZmineCore.getTaskExecutor().setCorePoolSize(threadPoolSize);
      }
    }

  }

}